WC HPC Software

Open HPC Community Software

The HPC software on the Fermilab WC cluster is packaged and distributed by the OpenHPC project. We are currently providing OpenHPC release v1.3 for Red Hat Enterprise 7.6.

Installed software components

Available software components are easily configured using the Lua lmod system which modifies the PATH and LD_LIBRARY_PATH (bash) shell environment variables and sets any other needed variables. Lmod also guards against a user having conflicting software packages (e.g. gnu8 compiler and an MPI built with clang) in your shell environment. More information on using lmod is available in the Introduction to lmod.

Quick introduction to using lmod

You can list all of the software components available using the spider option

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$ module spider   # (spyder is also acceptable spelling)
 

There is also an avail option, however, this option, unlike spider will only show available modules that do not conflict with your currently configured options. Assuming we do not have anything already configured with lmod, the avial option will display mainly the available compilers and other utilities that do not depend upon a particular compiler. Here is an (edited) example of the listing you will see:

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$ module avail
 ---------------------------- /opt/ohpc/pub/modulefiles ------------------------------
   EasyBuild/3.9.2       cmake/3.14.3    gnu8/8.3.0          llvm5/5.0.1    autotools
   autotools             gnu/5.4.0       hwloc/2.0.3         papi/5.7.0     singularity/3.2.1
   charliecloud/0.9.7    gnu7/7.3.0      intel/19.0.4.243    pmix/2.2.2     valgrind/3.15.0

The load command will enable a software package within your shell environment. If there is only a single
package version available, it suffices to use the package name, e.g. gnu8, without specifying the particular
version: gnu8/8.3.0. The following loads autotools, cmake, and gnu8:

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$ module load autotools cmake gnu8

Currently loaded modules can be displayed with list

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$ module list

Currently Loaded Modules:
  1) autotools   2) cmake/3.14.3   3) gnu8/8.3.0

If a package is no longer needed, it can be unloaded

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$ module unload autotools
$ module list

Currently Loaded Modules:
  1) cmake/3.14.3   2) gnu8/8.3.0

Running avail again will now show available modules that have gnu8 as a dependency

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$ module avail

--------------- /opt/ohpc/pub/moduledeps/gnu8 -----------------
   R/3.5.3        impi/2019.4.243    mpich/3.3         openblas/0.3.5    plasma/2.8.0        scotch/6.0.6
   gsl/2.5        likwid/4.3.4       mvapich2/2.3.1    openmpi3/3.1.4    py2-numpy/1.15.3    superlu/5.2.1
   hdf5/1.10.5    metis/5.1.0        ocr/1.0.1         pdtoolkit/3.25    py3-numpy/1.15.3

We can now load an MPI package

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$ module load openmpi3
$ module list

Currently Loaded Modules:
  1) cmake/3.14.3   2) gnu8/8.3.0   3) openmpi3/3.1.4

We can use swap to change to another MPI implementation

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$ module swap openmpi3 mvapich2
$ module list

Currently Loaded Modules:
  1) cmake/3.14.3   2) gnu8/8.3.0   3) mvapich2/2.3.1

The purge command will unload all current modules

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$ module purge
$ module list
No modules loaded

This is useful at the beginning of batch scripts to prevent the batch shell from unintentionally
inheriting a module environment from the submission shell.

Python3, Python2, and R conda environments

The supported python versions are provided by the anaconda project and available via the module system. To activate Python3, the base version of python do the following

$ module load anaconda3
$ conda activate

There is also a legacy Python2.7 version configurable as a conda environment. To activate Python2.7:

$ module load anaconda3
$ conda activate py27

To see a list of available system installed environments:

$ conda env list
# conda environments: 
base                     /srv/software/Anaconda3-2019.03
gnu-R                    /srv/software/Anaconda3 2019.03/envs/gnu-R
jax-cpu                  /srv/software/Anaconda3-2019.03/envs/jax-cpu
py27                  *  /srv/software/Anaconda3-2019.03/envs/py27

You are able to create your own local (to you) custom environments by either creating a new environment or starting by cloning and then customizing and existing environment.

Launching MPI processes

Near the beginning of your batch script, prior to launching an MPI process you should ensure only software modules required by the batch script have been loaded, for example if using gnu8 and openmpi:

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module purge
module load gnu8 openmpi3

There are two common mechanisms for starting up MPI either use ‘mpirun’ or ‘srun’. An ‘mpirun’ command is provided by each MPI implementation, and is specific to that implementation. The commands provided by openmpi, mvapich, and Intel impi are slurm “aware”. They will attempt to use slurm interfaces to distribute and start MPI binaries. In addition, slurm has the srun command that is able to startup MPI. The following command will list APIs ‘srun’ supports for MPI

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$ srun --mpi=list
srun: MPI types are...
srun: pmi2
srun: pmix_v3
srun: pmix
srun: none
srun: openmpi
srun: pmix_v2

The table below lists recommended launchers for the different MPI implementations. These combinations have been proved to work. Combinations that are not listed either fail, or do not properly launch MPI.

MPILauncher + any required Flags
openmpi3srun --mpi=pmix
openmpi3mpirun
mvpaich2srun --mpi=pmi2
mvapich2mpirun
impisrun --mpi=pmi2

We recommend using srun to launch all three MPI implementations since it is then possible to use command line options specify the distribution and binding of MPI ranks to CPU cores and local memory. The options are described in the srun documentation. Careful specification of the process affinities is especially important when running MPI in the hybrid approach combining MPI with thread parallelism. TU Dresden has a nice compendium illustrating different srundistribution and binding options for MPI.